setwd("/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/Conditions")
suppressPackageStartupMessages({
library(data.table)
library(DESeq2)
library(gplots)
library(here)
library(hyperSpec)
library(limma)
library(LSD)
library(magrittr)
library(matrixStats)
library(parallel)
library(pander)
library(plotly)
library(RColorBrewer)
library(scatterplot3d)
library(tidyverse)
library(tximport)
library(VennDiagram)
library(vsn)
})
suppressPackageStartupMessages({
source("~/Git/UPSCb/UPSCb-common/src/R/featureSelection.R")
source("~/Git/UPSCb/UPSCb-common/src/R/gopher.R")
source("~/Git/UPSCb/UPSCb-common/src/R/plot.multidensity.R")
source("~/Git/UPSCb/UPSCb-common/src/R/volcanoPlot.R")
})
lfc <- 0.5
FDR <- 0.01
pal <- c(brewer.pal(8,"Dark2"),1)
pal2 <- brewer.pal(9,"Paired") #require package RColorBrewer
cols <- rainbow(17)
hpal <- colorRampPalette(c("blue","white","red"))(100)
mar <- par("mar")
samples <- read.csv("~/Git/arabidopsis-nutrition-tor/doc/samples3.csv")
samples %<>% filter(!grepl("P11554_1",SciLifeID)) %>%
filter(! SciLifeID %in% c("P13406_101",
"P14066_128",
"P14066_133",
"P13406_102",
"P14066_131")) %>%
filter(! Nutrition == "PKS") %>%
mutate(Nutrition=relevel(as.factor(Nutrition),"NPS"),AZD=relevel(as.factor(AZD),"DMSO"))
samples <- samples[order(samples$Timepoint, samples$Nutrition, samples$AZD),]
samples %<>% mutate(Timepoint,Timepoint=factor(paste0("T",Timepoint)))
filenames <- list.files("../Salmon",
recursive = TRUE,
pattern = "quant.sf",
full.names = TRUE)
names(filenames) <- sub("_S.*","",sapply(strsplit(filenames, "/"), .subset, 3))
filenames <- filenames[match(samples$SciLifeID,names(filenames))]
filenames <-filenames[!is.na(names(filenames))]
samples <- samples[match(names(filenames),samples$SciLifeID),]
samples$Conditions <- factor(paste(samples$Timepoint,
samples$Nutrition,
samples$AZD,sep="_"),
levels=c("T0_T0_0",
"T6_NPS_DMSO", "T6_NPS_AZD", "T6_NS_DMSO", "T6_NS_AZD", "T6_NP_DMSO", "T6_NP_AZD",
"T24_NPS_DMSO", "T24_NPS_AZD", "T24_NS_DMSO", "T24_NS_AZD", "T24_NP_DMSO", "T24_NP_AZD"))
samples <- cbind(samples,
Id = gsub(".+-",
"",
samples$SampleName))
samples <- cbind(samples,
Tp_Id = factor(paste(samples$Timepoint,
samples$Id,
sep=".")))
write.csv(samples,"/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/samplelist.csv")
Read the expression at the transcript level
tx <- suppressMessages(tximport(files = filenames,
type = "salmon",
txOut = TRUE))
summarise to genes
tx2gene <- data.frame(TXID=rownames(tx$counts),
GENEID=sub("\\.[0-9]+","",rownames(tx$counts)))
gx <- summarizeToGene(tx,tx2gene=tx2gene)
## summarizing abundance
## summarizing counts
## summarizing length
kg <- round(gx$counts)
Sanity check
stopifnot(all(colnames(kg) == samples$SciLifeID))
#dir.create(file.path("analysis_Tom","salmon"),showWarnings=FALSE,recursive=TRUE)
#write.table(kg,file="/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/nutrition-unormalised-gene-expression_data.csv")
#save(kg, samples, file = "/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/counts.rda")
sel <- rowSums(kg) == 0
sprintf("%s%% (%s) of %s genes are not expressed",
round(sum(sel) * 100/ nrow(kg),digits=1),
sum(sel),
nrow(kg))
## [1] "17.9% (5793) of 32310 genes are not expressed"
For visualization, the data is submitted to a variance stabilization transformation using DESeq2. The dispersion is estimated independently of the sample type
dds <- DESeqDataSetFromMatrix(
countData = kg,
colData = samples,
design = ~ Conditions)
## converting counts to integer mode
dds <- estimateSizeFactors(dds)
vst <- varianceStabilizingTransformation(dds,blind=FALSE)
vsd <- assay(vst)
vsd <- vsd - min(vsd)
Write out
stopifnot(all(colnames(vsd) == samples$SciLifeID))
colnames(vsd) <- samples$Tp_Id
write.csv(vsd,"/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/library-size-normalized_variance-stabilized_data_nutrition.csv")
Principal Component Analysis on the normalized data * Establishment of the PCA
conditions1 <- factor(paste(samples$AZD,samples$Nutrition,sep="_"))
pc <- prcomp(t(vsd))
percent <- round(summary(pc)$importance[2,]*100);percent
## PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 PC14 PC15 PC16
## 43 24 13 6 4 2 1 1 1 1 0 0 0 0 0 0
## PC17 PC18 PC19 PC20 PC21 PC22 PC23 PC24 PC25 PC26 PC27 PC28 PC29 PC30 PC31 PC32
## 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
## PC33 PC34 PC35 PC36 PC37 PC38 PC39 PC40 PC41 PC42 PC43 PC44
## 0 0 0 0 0 0 0 0 0 0 0 0
conds <- droplevels(conditions1)
plot(pc$x[,1],
pc$x[,2],
xlab=paste("Comp. 1 (",percent[1],"%)",sep=""),
ylab=paste("Comp. 2 (",percent[2],"%)",sep=""),
col=pal[as.integer(conds)],
pch=c(15,16,17)[as.factor(samples$Timepoint)],
main="All timepoints")
legend("bottomright",pch=19,
col=pal[1:nlevels(conds)],
legend=levels(conds))
legend("topleft",pch=c(15,16,17),
col="black",
legend=c("T0","T6","T24"))
plot(pc$x[,2],
pc$x[,3],
xlab=paste("Comp. 2 (",percent[2],"%)",sep=""),
ylab=paste("Comp. 3 (",percent[3],"%)",sep=""),
col=pal[as.integer(conds)],
pch=c(15,16,17)[as.factor(samples$Timepoint)],
main="All timepoints")
legend("bottomleft",pch=19,
col=pal[1:nlevels(conds)],
legend=levels(conds))
legend("topleft",pch=c(15,16,17),
col="black",
legend=c("T0","T6","T24"))
plot(pc$x[,1],
pc$x[,3],
xlab=paste("Comp. 1 (",percent[1],"%)",sep=""),
ylab=paste("Comp. 3 (",percent[3],"%)",sep=""),
col=pal[as.integer(conds)],
pch=c(15,16,17)[as.factor(samples$Timepoint)],
main="All timepoints")
legend("bottomleft",pch=19,
col=pal[1:nlevels(conds)],
legend=levels(conds))
legend("bottomright",pch=c(15,16,17),
col="black",
legend=c("T0","T6","T24"))
sel <- samples$Timepoint %in% c("T0","T6","T24")
suppressMessages(dds <- DESeqDataSetFromMatrix(
countData = kg[,sel],
colData = samples[sel,],
design = ~ Conditions))
dds <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 2 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
vst <- varianceStabilizingTransformation(dds,blind=FALSE)
vsd <- assay(vst)
vsd <- vsd - min(vsd)
The contrast by default is the first one (not Intercept)
resultsNames(dds)
## [1] "Intercept" "Conditions_T6_NPS_DMSO_vs_T0_T0_0"
## [3] "Conditions_T6_NPS_AZD_vs_T0_T0_0" "Conditions_T6_NS_DMSO_vs_T0_T0_0"
## [5] "Conditions_T6_NS_AZD_vs_T0_T0_0" "Conditions_T6_NP_DMSO_vs_T0_T0_0"
## [7] "Conditions_T6_NP_AZD_vs_T0_T0_0" "Conditions_T24_NPS_DMSO_vs_T0_T0_0"
## [9] "Conditions_T24_NPS_AZD_vs_T0_T0_0" "Conditions_T24_NS_DMSO_vs_T0_T0_0"
## [11] "Conditions_T24_NS_AZD_vs_T0_T0_0" "Conditions_T24_NP_DMSO_vs_T0_T0_0"
## [13] "Conditions_T24_NP_AZD_vs_T0_T0_0"
res <- results(dds,name = "Conditions_T6_NPS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NPS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9664 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5302 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4362 genes that are repressed
res <- results(dds,name = "Conditions_T6_NPS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NPS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 8735 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4639 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4096 genes that are repressed
res <- results(dds,name = "Conditions_T6_NS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 6589 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 3553 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3036 genes that are repressed
res <- results(dds,name = "Conditions_T6_NS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9218 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4775 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4443 genes that are repressed
res <- results(dds,name = "Conditions_T6_NP_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NP_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9491 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5053 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4438 genes that are repressed
res <- results(dds,name = "Conditions_T6_NP_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NP_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 7818 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4332 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3486 genes that are repressed
res <- results(dds,name = "Conditions_T24_NPS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NPS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 10531 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5150 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 5381 genes that are repressed
res <- results(dds,name = "Conditions_T24_NPS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NPS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 8349 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4066 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4283 genes that are repressed
res <- results(dds,name = "Conditions_T24_NS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 4579 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 2165 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 2414 genes that are repressed
res <- results(dds,name = "Conditions_T24_NS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 7102 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 3258 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3844 genes that are repressed
res <- results(dds,name = "Conditions_T24_NP_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NP_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9502 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4685 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4817 genes that are repressed
res <- results(dds,name = "Conditions_T24_NP_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NP_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR
message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 8906 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4614 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4292 genes that are repressed
levels(samples$Conditions)
## [1] "T0_T0_0" "T6_NPS_DMSO" "T6_NPS_AZD" "T6_NS_DMSO" "T6_NS_AZD"
## [6] "T6_NP_DMSO" "T6_NP_AZD" "T24_NPS_DMSO" "T24_NPS_AZD" "T24_NS_DMSO"
## [11] "T24_NS_AZD" "T24_NP_DMSO" "T24_NP_AZD"
sel_T0 <- samples$Timepoint %in% c("T0","T6","T24")
suppressMessages(dds_T0 <- DESeqDataSetFromMatrix(
countData = kg[,sel_T0],
colData = samples[sel_T0,],
design = ~ Conditions))
dds_T0 <- DESeq(dds_T0)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 2 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
vst_T0 <- varianceStabilizingTransformation(dds_T0,blind=FALSE)
vsd_T0 <- assay(vst_T0)
vsd_T0 <- vsd_T0 - min(vsd_T0)
sel1 <- rownames(vsd_T0)
expr <- vsd_T0[match(sel1,rownames(vsd_T0)),]
Avg <- sapply(split.data.frame(t(expr),
f = droplevels(samples$Conditions[sel_T0])),
colMeans)
SD <- sapply(split.data.frame(t(expr),f = droplevels(samples$Conditions[sel_T0])),colSds)
rownames(SD) <- rownames(Avg)
write.table(Avg, file = "Averaged_Normalized_Counts.csv", sep = ";", row.names = FALSE, dec=",")
write.table(rownames(Avg), file = "Averaged_Normalized_Counts_genes.csv", sep = ";", row.names = FALSE, dec=",")
sel1 <- c("AT1G50030","AT3G18140","AT2G22040","AT3G08850","AT5G01770")
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1,ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
for (i in 1:length(AvgTOR[,1])){
barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i],ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.2,code=3)
}
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
for (i in 1:length(AvgTOR[,1]))
{
a[1:6,1] <- AvgTOR[i,1]
a[1:6,2] <- AvgTOR[i,2:7]
a[1:6,3] <- AvgTOR[i,8:13]
b[1:6,1] <- SDTOR[i,1]
b[1:6,2] <- SDTOR[i,2:7]
b[1:6,3] <- SDTOR[i,8:13]
plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[1,] - b[1,],
y1=a[1,] + b[1,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[2,] - b[2,],
y1=a[2,] + b[2,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[3,] - b[3,],
y1=a[3,] + b[3,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[4,] - b[4,],
y1=a[4,] + b[4,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[5,] - b[5,],
y1=a[5,] + b[5,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[6,] - b[6,],
y1=a[6,] + b[6,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -0.5] <- -0.5; AvgTOR_norm[AvgTOR_norm > 0.5] <- 0.5
heatmap.2(AvgTOR_norm,
col=hpal,
dendrogram="none",
trace="none",
Colv=FALSE,
Rowv=FALSE,
margins=c(8,12))
sel1 <- c("AT1G50030","AT3G18140","AT3G08850","AT5G01770")
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
TOR <- vsd_T0[match(sel1,rownames(vsd_T0)),]
TOR_norm <- TOR/AvgTOR[,1]
TOR_norm <- log2(TOR_norm)
colnames(TOR_norm) <- samples$Conditions
a <- match(colnames(TOR_norm),samples$Conditions)
plot(TOR_norm[4,] ~ a, ylim=c(-0.5,0.5),main="AT5G01770")
b <- c(1,9,12,21,24,15,18,27,30,39,42,33,36)
lines(b,AvgTOR_norm[5,])
sel1 <- read.csv("~/arabidopsis-nutrition-TOR/seidr/cell_cycle_genes.csv", sep=";")[,1]
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1,ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
for (i in 1:length(AvgTOR[,1]))
{
a[1:6,1] <- AvgTOR[i,1]
a[1:6,2] <- AvgTOR[i,2:7]
a[1:6,3] <- AvgTOR[i,8:13]
b[1:6,1] <- SDTOR[i,1]
b[1:6,2] <- SDTOR[i,2:7]
b[1:6,3] <- SDTOR[i,8:13]
plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[1,] - b[1,],
y1=a[1,] + b[1,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[2,] - b[2,],
y1=a[2,] + b[2,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[3,] - b[3,],
y1=a[3,] + b[3,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[4,] - b[4,],
y1=a[4,] + b[4,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[5,] - b[5,],
y1=a[5,] + b[5,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[6,] - b[6,],
y1=a[6,] + b[6,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3
heatmap.2(AvgTOR_norm,
col=hpal,
dendrogram="none",
trace="none",
Colv=FALSE,
Rowv=FALSE,
margins=c(8,8),
labRow = read.csv("~/arabidopsis-nutrition-TOR/seidr/cell_cycle_genes.csv", sep=";")[,2])
heatmap.2(AvgTOR_norm,
trace="none",
col=hpal,
Colv=FALSE,
dendrogram = "row",
labRow = read.csv("~/arabidopsis-nutrition-TOR/seidr/cell_cycle_genes.csv", sep=";")[,2],
margins=c(8,8),
hclustfun = function(X){hclust(X,method="ward.D2")})
sel1 <- c("AT5G65360","AT1G09200","AT3G27360","AT5G10400","AT5G65350","AT5G10390","AT4G40030",
"AT4G40040","AT5G10980","AT1G13370","AT1G75600","AT1G01370")
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
for (i in 1:length(AvgTOR[,1])){
barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.2,code=3)
}
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
for (i in 1:length(AvgTOR[,1]))
{
a[1:6,1] <- AvgTOR[i,1]
a[1:6,2] <- AvgTOR[i,2:7]
a[1:6,3] <- AvgTOR[i,8:13]
b[1:6,1] <- SDTOR[i,1]
b[1:6,2] <- SDTOR[i,2:7]
b[1:6,3] <- SDTOR[i,8:13]
plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[1,] - b[1,],
y1=a[1,] + b[1,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[2,] - b[2,],
y1=a[2,] + b[2,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[3,] - b[3,],
y1=a[3,] + b[3,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[4,] - b[4,],
y1=a[4,] + b[4,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[5,] - b[5,],
y1=a[5,] + b[5,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[6,] - b[6,],
y1=a[6,] + b[6,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}
AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3
heatmap.2(AvgTOR_norm,
col=hpal,
dendrogram="none",
trace="none",
Colv=FALSE,
Rowv=FALSE,
margins=c(8,12))
sel1 <- c("AT5G43350","AT5G43370","AT5G43360","AT2G38940","AT2G32830","AT5G43340","AT3G54700",
"AT1G20860","AT1G76430","AT3G26570","AT5G14040","AT3G48850","AT2G17270","AT5G46110",
"AT5G33320","AT5G54800","AT1G61800","AT5G17640","AT1G73010","AT1G17710",
"AT3G09922" ,"AT2G02990","AT3G17790")
sel1 <- c("AT5G43350","AT5G43370","AT5G43360","AT2G38940","AT2G32830","AT5G43340","AT3G54700",
"AT1G20860","AT1G76430","AT3G26570","AT5G14040","AT3G48850","AT2G17270","AT5G46110",
"AT5G33320","AT5G54800","AT1G61800","AT5G17640","AT1G73010","AT1G17710")
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
for (i in 1:length(AvgTOR[,1])){
barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.2,code=3)
}
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
for (i in 1:length(AvgTOR[,1]))
{
a[1:6,1] <- AvgTOR[i,1]
a[1:6,2] <- AvgTOR[i,2:7]
a[1:6,3] <- AvgTOR[i,8:13]
b[1:6,1] <- SDTOR[i,1]
b[1:6,2] <- SDTOR[i,2:7]
b[1:6,3] <- SDTOR[i,8:13]
plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[1,] - b[1,],
y1=a[1,] + b[1,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[2,] - b[2,],
y1=a[2,] + b[2,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[3,] - b[3,],
y1=a[3,] + b[3,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[4,] - b[4,],
y1=a[4,] + b[4,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[5,] - b[5,],
y1=a[5,] + b[5,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[6,] - b[6,],
y1=a[6,] + b[6,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3
heatmap.2(AvgTOR_norm,
col=hpal,
dendrogram="none",
trace="none",
Colv=FALSE,
Rowv=FALSE,
margins=c(8,12))
sel1 <- c('AT5G01220','AT3G02870','AT3G17790','AT5G64000','AT3G52820','AT2G11810','AT1G73010',
'AT3G03540','AT3G02040','AT5G20410','AT3G05630','AT4G33030','AT2G27190','AT4G00550',
'AT2G45130','AT5G20150','AT2G26660','AT1G68740','AT2G32830','AT2G38940','AT1G20860',
'AT3G58810','AT5G56080','AT5G04950','AT1G23020','AT4G19690','AT3G46900','AT4G19680',
'AT1G09790','AT3G58060','AT5G03570','AT2G28160','AT2G03260','AT1G74770','AT4G09110',
'AT5G06490','AT1G49390','AT1G72200','AT2G35000','AT3G12900','AT4G30120')
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
for (i in 1:length(AvgTOR[,1])){
barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.2,code=3)
}
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
for (i in 1:length(AvgTOR[,1]))
{
a[1:6,1] <- AvgTOR[i,1]
a[1:6,2] <- AvgTOR[i,2:7]
a[1:6,3] <- AvgTOR[i,8:13]
b[1:6,1] <- SDTOR[i,1]
b[1:6,2] <- SDTOR[i,2:7]
b[1:6,3] <- SDTOR[i,8:13]
plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[1,] - b[1,],
y1=a[1,] + b[1,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[2,] - b[2,],
y1=a[2,] + b[2,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[3,] - b[3,],
y1=a[3,] + b[3,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[4,] - b[4,],
y1=a[4,] + b[4,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[5,] - b[5,],
y1=a[5,] + b[5,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[6,] - b[6,],
y1=a[6,] + b[6,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped
AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3
heatmap.2(AvgTOR_norm,
col=hpal,
dendrogram="none",
trace="none",
Colv=FALSE,
Rowv=FALSE,
margins=c(8,12))
sel1 <- c('AT2G03090','AT3G10950','AT3G25250','AT4G30280','AT5G13210','AT5G65110','AT1G12780','AT4G02520','AT3G12970','AT3G47540',
'AT4G11650','AT4G30490','AT2G29490','AT2G38870','AT3G45970','AT5G22920','AT5G39320','AT1G75380','AT5G39580','AT5G57655',
'AT1G54100','AT1G68440','AT1G76870','AT2G33150','AT3G04720','AT3G44300','AT3G59270','AT1G51400','AT2G30860','AT3G28180',
'AT4G37610','AT5G07440','AT5G49360')
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped
for (i in 1:length(AvgTOR[,1])){
barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.2,code=3)
}
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped
a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
for (i in 1:length(AvgTOR[,1]))
{
a[1:6,1] <- AvgTOR[i,1]
a[1:6,2] <- AvgTOR[i,2:7]
a[1:6,3] <- AvgTOR[i,8:13]
b[1:6,1] <- SDTOR[i,1]
b[1:6,2] <- SDTOR[i,2:7]
b[1:6,3] <- SDTOR[i,8:13]
plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[1,] - b[1,],
y1=a[1,] + b[1,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[2,] - b[2,],
y1=a[2,] + b[2,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[3,] - b[3,],
y1=a[3,] + b[3,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[4,] - b[4,],
y1=a[4,] + b[4,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[5,] - b[5,],
y1=a[5,] + b[5,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[6,] - b[6,],
y1=a[6,] + b[6,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3
heatmap.2(AvgTOR_norm,
col=hpal,
dendrogram="none",
trace="none",
Colv=FALSE,
Rowv=FALSE,
margins=c(8,12))
sel1 <- c("AT1G04810","AT1G09100","AT1G45000","AT1G53750","AT1G64520","AT2G20140","AT2G20580",
"AT2G32730","AT3G05530","AT4G19006","AT4G24820","AT4G28470","AT4G29040","AT4G38630",
"AT5G05780","AT5G09900","AT5G19990","AT5G20000","AT5G43010","AT5G45620","AT5G58290",
"AT5G64760")
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1,ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
for (i in 1:length(AvgTOR[,1])){
barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i],ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.2,code=3)
}
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
for (i in 1:length(AvgTOR[,1]))
{
a[1:6,1] <- AvgTOR[i,1]
a[1:6,2] <- AvgTOR[i,2:7]
a[1:6,3] <- AvgTOR[i,8:13]
b[1:6,1] <- SDTOR[i,1]
b[1:6,2] <- SDTOR[i,2:7]
b[1:6,3] <- SDTOR[i,8:13]
plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[1,] - b[1,],
y1=a[1,] + b[1,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[2,] - b[2,],
y1=a[2,] + b[2,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[3,] - b[3,],
y1=a[3,] + b[3,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[4,] - b[4,],
y1=a[4,] + b[4,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[5,] - b[5,],
y1=a[5,] + b[5,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[6,] - b[6,],
y1=a[6,] + b[6,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}
AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -0.5] <- -0.5; AvgTOR_norm[AvgTOR_norm > 0.5] <- 0.5
heatmap.2(AvgTOR_norm,
col=hpal,
dendrogram="none",
trace="none",
Colv=FALSE,
Rowv=FALSE,
margins=c(8,12))
heatmap.2(AvgTOR_norm,
col=hpal,
dendrogram="row",
trace="none",
Colv=FALSE,
margins=c(8,12),
hclustfun = function(X){hclust(X,method="ward.D2")})
sel1 <- c("AT1G13060","AT1G16470","AT1G21720","AT1G47250","AT1G53850","AT1G56450","AT1G77440",
"AT2G05840","AT2G27020","AT3G14290","AT3G22110","AT3G22630","AT3G27430","AT3G51260",
"AT3G60820","AT4G14800","AT4G31300","AT5G35590","AT5G40580","AT5G66140")
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]
barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1,ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
lwd=1.5, angle=90, length=0.05,code=3)
for (i in 1:length(AvgTOR[,1])){
barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i],ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.2,code=3)
}
for (i in 1:length(AvgTOR[,1]))
{
plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
lwd=1.5, angle=90, length=0.05,code=3)
}
a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
for (i in 1:length(AvgTOR[,1]))
{
a[1:6,1] <- AvgTOR[i,1]
a[1:6,2] <- AvgTOR[i,2:7]
a[1:6,3] <- AvgTOR[i,8:13]
b[1:6,1] <- SDTOR[i,1]
b[1:6,2] <- SDTOR[i,2:7]
b[1:6,3] <- SDTOR[i,8:13]
plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[1,] - b[1,],
y1=a[1,] + b[1,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[2,] - b[2,],
y1=a[2,] + b[2,],
lwd=1, angle=90, length=0.05, code=3)
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[3,] - b[3,],
y1=a[3,] + b[3,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[4,] - b[4,],
y1=a[4,] + b[4,],
lwd=1, angle=90, length=0.05, code=3, col="turquoise")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[5,] - b[5,],
y1=a[5,] + b[5,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
arrows(x0=c(0,6,24),
x1=c(0,6,24),
y0=a[6,] - b[6,],
y1=a[6,] + b[6,],
lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}
AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -0.5] <- -0.5; AvgTOR_norm[AvgTOR_norm > 0.5] <- 0.5
heatmap.2(AvgTOR_norm,
col=hpal,
dendrogram="none",
trace="none",
Colv=FALSE,
Rowv=FALSE,
margins=c(8,12))
heatmap.2(AvgTOR_norm,
col=hpal,
dendrogram="row",
trace="none",
Colv=FALSE,
margins=c(8,12),
hclustfun = function(X){hclust(X,method="ward.D2")})
sel1 <- c("AT1G05205","AT1G47840","AT1G47845","AT2G19860","AT4G29130")
sel1 <- c("AT1G47845","AT4G29130")
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] vsn_3.58.0 VennDiagram_1.6.20
## [3] futile.logger_1.4.3 tximport_1.18.0
## [5] forcats_0.5.0 stringr_1.4.0
## [7] dplyr_1.0.2 purrr_0.3.4
## [9] readr_1.4.0 tidyr_1.1.2
## [11] tibble_3.0.4 tidyverse_1.3.0
## [13] scatterplot3d_0.3-41 RColorBrewer_1.1-2
## [15] plotly_4.9.2.1 pander_0.6.3
## [17] magrittr_2.0.1 LSD_4.1-0
## [19] limma_3.46.0 hyperSpec_0.99-20200527
## [21] xml2_1.3.2 ggplot2_3.3.2
## [23] lattice_0.20-41 here_1.0.0
## [25] gplots_3.1.0 DESeq2_1.30.0
## [27] SummarizedExperiment_1.20.0 Biobase_2.50.0
## [29] MatrixGenerics_1.2.0 matrixStats_0.57.0
## [31] GenomicRanges_1.42.0 GenomeInfoDb_1.26.1
## [33] IRanges_2.24.0 S4Vectors_0.28.0
## [35] BiocGenerics_0.36.0 data.table_1.13.2
##
## loaded via a namespace (and not attached):
## [1] colorspace_2.0-0 ellipsis_0.3.1 rprojroot_2.0.2
## [4] XVector_0.30.0 fs_1.5.0 rstudioapi_0.13
## [7] affyio_1.60.0 bit64_4.0.5 fansi_0.4.1
## [10] AnnotationDbi_1.52.0 lubridate_1.7.9.2 splines_4.0.3
## [13] geneplotter_1.68.0 knitr_1.30 jsonlite_1.7.1
## [16] broom_0.7.2 annotate_1.68.0 dbplyr_2.0.0
## [19] png_0.1-7 BiocManager_1.30.10 compiler_4.0.3
## [22] httr_1.4.2 backports_1.2.0 assertthat_0.2.1
## [25] Matrix_1.2-18 lazyeval_0.2.2 cli_2.2.0
## [28] formatR_1.7 htmltools_0.5.0 tools_4.0.3
## [31] affy_1.68.0 gtable_0.3.0 glue_1.4.2
## [34] GenomeInfoDbData_1.2.4 Rcpp_1.0.5 cellranger_1.1.0
## [37] vctrs_0.3.5 preprocessCore_1.52.0 xfun_0.19
## [40] testthat_3.0.0 rvest_0.3.6 lifecycle_0.2.0
## [43] gtools_3.8.2 XML_3.99-0.5 zlibbioc_1.36.0
## [46] scales_1.1.1 hms_0.5.3 lambda.r_1.2.4
## [49] yaml_2.2.1 memoise_1.1.0 latticeExtra_0.6-29
## [52] stringi_1.5.3 RSQLite_2.2.1 highr_0.8
## [55] genefilter_1.72.0 caTools_1.18.0 BiocParallel_1.24.1
## [58] rlang_0.4.9 pkgconfig_2.0.3 bitops_1.0-6
## [61] evaluate_0.14 htmlwidgets_1.5.2 bit_4.0.4
## [64] tidyselect_1.1.0 R6_2.5.0 generics_0.1.0
## [67] DelayedArray_0.16.0 DBI_1.1.0 pillar_1.4.7
## [70] haven_2.3.1 withr_2.3.0 survival_3.2-7
## [73] RCurl_1.98-1.2 modelr_0.1.8 crayon_1.3.4
## [76] futile.options_1.0.1 KernSmooth_2.23-18 rmarkdown_2.5
## [79] jpeg_0.1-8.1 locfit_1.5-9.4 readxl_1.3.1
## [82] blob_1.2.1 reprex_0.3.0 digest_0.6.27
## [85] xtable_1.8-4 munsell_0.5.0 viridisLite_0.3.0